The elongation cycle of protein synthesis is driven by two elongation factors that bind to nearly identical sites on the large (50S) ribosomal subunit (Spahn and Nierhaus, 1998; Wilson and Noller, 1998). EF-Tu delivers aminoacyl tRNAs to the ribosome, whereas EF-G catalyzes the translocation of the ribosome by one codon relative to the mRNA and the concomitant movement of the A and P site tRNAs. Both elongation factors are G proteins, and their interactions with the ribosome are coupled to the binding and hydrolysis of GTP. Like most G proteins, EF-Tu and EF-G are molecular switches that have limited inherent GTPase activity, and they rely on an accessory factor to stimulate activity at the appropriate time. This accessory factor is an integral part of the 50S ribosomal subunit and has usually been referred to as the “GTPase center,” but by analogy with the functionally equivalent GAP proteins that stimulate GTPase activity in G-proteins, it seems more appropriate to refer to it as the “GTPase activating region” (hereafter abbreviated as the GAR). Early work on the identification of the molecular components of the GAR implicated a complex between ribosomal protein L11 and a highly conserved 58-nucleotide stretch of 23S ribosomal RNA (rRNA), nucleotides 1051-1108 in Escherichia coli (Schmidt et al., 1981; Thompson et al., 1979). The L11-RNA complex is the target for a family of thiazole antibiotics that includes thiostrepton and micrococcin. Thiostrepton binds essentially irreversibly to 50S subunits (Sopori and Lengyel, 1972) and inhibits hydrolysis of GTP by EF-G (Pestka, 1970; Rodnina et al., 1997), while micrococcin binds to the same complex and stimulates GTP hydrolysis by EF-G (Cundliffe and Thompson, 1981).
Other components of the ribosome have also been implicated in stimulation of GTP hydrolysis by elongation factors. Classical work suggested that protein L7/L12, which together with L10 forms the “stalk” of the 50S subunit that lies adjacent to L11, is involved in stimulation of GTPase activity in EF-Tu (Donner et al., 1978). However, recently it has been shown that protein L7/L12, although essential for stalk formation, is not required for viability in yeast (Briones et al., 1998). The sarcin/ricin loop, a small, highly conserved stem-loop in the 23S rRNA that is known to be essential for ribosome function, has been footprinted by the elongation factors (Moazed et al., 1988), and is also considered a candidate for being part of the GAR. Therefore, it is not yet clear whether the L11-RNA complex per se should be considered the GAR, or whether the GAR should be defined as a more extensive region of the 50S subunit. In any event, it appears that the L11-RNA complex is at the heart of the GAR; the complex of L11 with its cognate RNA will be referred to herein as the GAR.
The GAR is one of the most thoroughly characterized RNA-protein complexes. The secondary structure of the RNA was first inferred from biochemical and genetic studies (Glotz et al., 1981; Noller et al., 1981). It consists of a junction of four double-helical stems (FIG. 1A). Approximately one-third of the residues in the GAR RNA are very highly conserved. The structure, thermodynamic stability, and ion-binding affinities of the RNA component have been extensively probed by a variety of biophysical and biochemical techniques; these data suggest that the 1067 and 1095 stem-loops are folded into a compact tertiary structure (Conn et al., 1998; Rosendahl and Douthwaite, 1994). Protein L11 consists of two domains: the C-terminal domain binds tightly to the RNA tertiary structure, while the N-terminal domain is required for the cooperative interaction with thiostrepton (Xing and Draper, 1996). The structure of the C-terminal domain has been determined by NMR techniques (Hinck et al., 1997; Markus et al., 1997). Footprinting studies (Rosendahl and Douthwaite, 1993) have identified regions of RNA involved in the interaction with L11, while NMR chemical shift measurements (Hinck et al., 1997) have identified an RNA-binding surface on the C-terminal domain of the protein.
It is an object of the invention to provide a detailed view of a functionally important protein-RNA complex in the ribosome.
It is also an object of the invention to provide a high-resolution structure of a ribosomal protein-RNA complex.
Yet another object of the invention is to provide new principles of RNA folding, of RNA-protein recognition, and of indirect RNA tertiary structure stabilization.
Yet another object of the invention is to solve the three dimensional structure of L11 complexed with GAR RNA and to determine its structure coordinates.